Village Creek, located in Albany, California, is the lower tributary of Marin Creek. In 1998, the University of California at Berkeley daylighted a 900-foot stretch of the Creek and restored it to an 1,125 feet long open channel flanked by 0.77 acres of riparian and aquatic habitat. The objective of the project was to increase aquatic habitat, provide conveyance for a 100-year flood, and recreate the natural stream dimensions for a bankfull channel, floodplain, and upper bank. This appraisal evaluates the current hydraulic and geomorphological conditions to determine the change from initial implementation and design. The study of the newly formed channel complexity showed changes in gravel and sand bars, as well as pools, riffles, and glides. A comparison between the current state of the creek and the intended design allowed the determination of extent to which the restoration meets the intended goals. Longitudinal and cross-sectional surveys along with channel mapping revealed an increase channel complexity and minor changes in the channel shape. In addition, an evaluation of the vegetation shows significant improvement in the riparian habitat. However, there was no observed development in aquatic habitat in Village Creek.

אָשר שטשוטשינקסקי׃ סילועטן (דערציילונג)

Selection can result in populations becoming more adapted, yet even in the presence of selection other effects can constrain adaptation. Two of the effects that can cause this discrepancy are genotype by environment interactions (GxE) and the accumulation of deleterious alleles. GxE is observed when an allele has different effects depending on the environment and can result in the maintenance of genetic variation, particularly when no genotype is best adapted to all environments. Deleterious alleles are generally considered as those which are deleterious across the conditions members of a species might encounter. Although they experience negative selection, they can still contribute a substantial proportion of genetic variance.

In this dissertation, I analyzed GxE and deleterious alleles in maize. First, I investigated GxE in a maize mapping population. We find that GxE contributes a substantial amount to the phenotypic variance for many traits. While we identify loci contributing to GxE, overall most of the GxE variance may be due to unidentified polygenic effects. Estimating the genetic covariances between traits in each environment reveals large differences in the genetic variance-covariance matrix between environments and in particular shows that differences in selection on flowering time may be contributing to the observed GxE for yield. Second, we analyzed the distribution of structural variants in maize inbred lines along the genome. We find that structural variants are more depleted in constrained regions of the genome than single nucleotide polymorphisms, possibly indicating that structural variants are more likely to be deleterious. Finally, we apply a machine learning method to identify constrained regions of the maize genome based on population genetic data. These predictions allow us to assess more recent evolutionary constraint in maize and find regions where mutations are more likely to be deleterious.